Trajectory-Based Simulation of EPR Spectra: Models of Rotational Motion for Spin Labels on Proteins

Abstract

Direct time-domain simulation of continuous-wave (CW) EPR spectra from molecular dynamics (MD) trajectories has become increasingly popular, especially for proteins labeled with nitroxide spin labels. Due to the time-consuming nature of simulating adequately long MD trajectories, two approximate methods have been developed to reduce the MD trajectory length required for modeling EPR spectra: hindered Brownian diffusion (HBD) and hidden Markov models (HMMs). Here, we assess the accuracy of these two approximate methods relative to direct simulations from MD trajectories for three spin-labeled protein systems (a simple helical peptide, a soluble protein, and a membrane protein) and two nitroxide spin labels with differing mobilities (R1 and TOAC). We find that the HMMs generally outperform HBD. Although R1 dynamics partially resembles hindered Brownian diffusion (HBD), HMMs accommodate the multiple dynamic timescales for the transitions between rotameric states of R1 that cannot be captured accurately by a HBD model, even when a three-angle orientational potential and recently developed estimation methods for the rotational diffusion tensor are utilized. We show that TOAC dynamics closely resembles slow multi-site exchange between twist-boat and chair ring puckering states, and we establish for the first time that this motion is modeled well by a HMM with up to four states, but not by HBD. All MD trajectory data processing, stochastic trajectory simulations, and CW EPR spectral simulations are implemented in EasySpin, a free software package for MATLAB.

Clustering of Stearic Acids in Model Phospholipid Membranes Revealed by Double Electron–Electron Resonance

“…CW EPR spectra at room temperature (see Figure ) show a noticeable splitting of the high-field component for the 16-DSA concentrations varying in the interval between 0.5 and 2 mol %. This splitting is typical for anisotropic motion of the spin-labeled molecules, which was experimentally detected and/or theoretically simulated in a number of studiessee, e.g., refs − . However, when 16-DSA concentration is decreased below 0.5 mol %down to 0.25 mol %this splitting in Figure disappears.…”

Monitoring Protein–Protein Interactions in the Cyanobacterial Circadian Clock in Real Time via Electron Paramagnetic Resonance Spectroscopy

“…Nevertheless, considering the potential of SDSL–EPR in resolving multiple species in real time by using magnetic field as the second abscissa, its application could be extended if this barrier in site design is lowered. We envision that future researchers should be able to design SDSL–EPR probe sites based on molecular dynamics (MD) simulations. − To that end, multiple strategies have been implemented to directly compute the cw-EPR spectra of spin-labeled proteins from MD simulations. − However, screening of multiple sites via a full MD simulation can be computationally demanding. Alternatively, rotamer libraries have previously been computed for multiple nitroxide spin-labels as coarse-grain approximations to the true dynamics of the nitroxide moiety to aid in designing probe sites for favorable distance measurements. , Computed within the rotamer library-based calculations are metrics such as nitroxide partition function Z , which measures the tightness of the site and root-mean-square deviation of the midpoint of the N–O group from the mean position, both of which might be correlated with nitroxide mobility.…”

Combining Experimental Data and Computational Methods for the Non-Computer Specialist

“…These calculations are often difficult and provide mostly local information. More recently, several methods to simulate the complete EPR spectra using the MD trajectory have been developed [ 107 , 108 ]. Nevertheless, a breakthrough into the conformational computational techniques to understand fluctuation has been achieved using double electron–electron resonance (DEER) spectroscopy (also known as pulsed electron-electron double resonance) [ 109 ].…”